3.RNA. Engram and AD signatures
Cesar Sierra
2025-04-10
#To load image with all the analyses below done
Ploting
Engrams + NE together
2D
3D
Quantify
ANOVA with euclidean distances
## Group infected N euclidean_distance sd se ci
## 1 AD_GFP Neg 3793 7.039275 3.716410 0.06034374 0.1183093
## 2 AD_GFP Pos 1532 4.684451 3.872973 0.09894983 0.1940915
## 3 AD_OSK Neg 4417 7.482256 3.657594 0.05503409 0.1078944
## 4 AD_OSK Pos 1213 4.723786 3.847787 0.11047922 0.2167518
## 5 CON_GFP Neg 4545 6.853849 3.592678 0.05329069 0.1044757
## 6 CON_GFP Pos 1562 4.163874 3.009446 0.07614581 0.1493589## Df Sum Sq Mean Sq F value Pr(>F)
## infected 1 22100 22100 1674.143 <2e-16 ***
## Group 2 1116 558 42.273 <2e-16 ***
## infected:Group 2 99 49 3.745 0.0237 *
## Residuals 17056 225149 13
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = euclidean_distance ~ infected * Group, data = cell_meta_2)
##
## $infected
## diff lwr upr p adj
## Pos-Neg -2.619871 -2.745376 -2.494365 0
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP 0.3368662 0.1740759 0.4996566 0.0000037
## CON_GFP-AD_GFP -0.2796102 -0.4392803 -0.1199400 0.0001205
## CON_GFP-AD_OSK -0.6164764 -0.7738192 -0.4591336 0.0000000
##
## $`infected:Group`
## diff lwr upr p adj
## Pos:AD_GFP-Neg:AD_GFP -2.35482376 -2.6682857 -2.0413619 0.0000000
## Neg:AD_OSK-Neg:AD_GFP 0.44298183 0.2137567 0.6722069 0.0000006
## Pos:AD_OSK-Neg:AD_GFP -2.31548856 -2.6570504 -1.9739267 0.0000000
## Neg:CON_GFP-Neg:AD_GFP -0.18542560 -0.4131546 0.0423034 0.1856914
## Pos:CON_GFP-Neg:AD_GFP -2.87540045 -3.1867108 -2.5640901 0.0000000
## Neg:AD_OSK-Pos:AD_GFP 2.79780558 2.4907799 3.1048312 0.0000000
## Pos:AD_OSK-Pos:AD_GFP 0.03933519 -0.3586411 0.4373114 0.9997623
## Neg:CON_GFP-Pos:AD_GFP 2.16939816 1.8634879 2.4753084 0.0000000
## Pos:CON_GFP-Pos:AD_GFP -0.52057669 -0.8929135 -0.1482398 0.0009585
## Pos:AD_OSK-Neg:AD_OSK -2.75847039 -3.0941352 -2.4228055 0.0000000
## Neg:CON_GFP-Neg:AD_OSK -0.62840743 -0.8471924 -0.4096224 0.0000000
## Pos:CON_GFP-Neg:AD_OSK -3.31838227 -3.6232109 -3.0135536 0.0000000
## Neg:CON_GFP-Pos:AD_OSK 2.13006296 1.7954180 2.4647079 0.0000000
## Pos:CON_GFP-Pos:AD_OSK -0.55991188 -0.9561957 -0.1636281 0.0008052
## Pos:CON_GFP-Neg:CON_GFP -2.68997485 -2.9936801 -2.3862696 0.0000000## Df Sum Sq Mean Sq F value Pr(>F)
## Group 2 289 144.57 11.3 1.27e-05 ***
## Residuals 4304 55047 12.79
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = euclidean_distance ~ Group, data = cell_meta_pos)
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP 0.03933519 -0.2829154 0.3615858 0.9558587
## CON_GFP-AD_GFP -0.52057669 -0.8220664 -0.2190869 0.0001553
## CON_GFP-AD_OSK -0.55991188 -0.8807920 -0.2390317 0.0001295MANOVA
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 5 0.93352 79.194 15 47079 < 2.2e-16 ***
## Residuals 17056
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $`Pos.AD_OSK vs Pos.CON_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.98853 10.713 3 2771 5.338e-07 ***
## Residuals 2773
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.AD_OSK vs Pos.AD_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.98318 15.635 3 2741 4.402e-10 ***
## Residuals 2743
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.AD_OSK vs Neg.AD_OSK`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.94247 114.47 3 5626 < 2.2e-16 ***
## Residuals 5628
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.AD_OSK vs Neg.CON_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.96179 76.195 3 5754 < 2.2e-16 ***
## Residuals 5756
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.AD_OSK vs Neg.AD_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.96471 60.986 3 5002 < 2.2e-16 ***
## Residuals 5004
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.CON_GFP vs Pos.AD_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.9521 51.822 3 3090 < 2.2e-16 ***
## Residuals 3092
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.CON_GFP vs Neg.AD_OSK`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.92461 162.39 3 5975 < 2.2e-16 ***
## Residuals 5977
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.CON_GFP vs Neg.CON_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.94729 113.19 3 6103 < 2.2e-16 ***
## Residuals 6105
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.CON_GFP vs Neg.AD_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.94466 104.48 3 5351 < 2.2e-16 ***
## Residuals 5353
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.AD_GFP vs Neg.AD_OSK`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.90591 205.82 3 5945 < 2.2e-16 ***
## Residuals 5947
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.AD_GFP vs Neg.CON_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.94028 128.56 3 6073 < 2.2e-16 ***
## Residuals 6075
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Pos.AD_GFP vs Neg.AD_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.9355 122.28 3 5321 < 2.2e-16 ***
## Residuals 5323
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Neg.AD_OSK vs Neg.CON_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.99211 23.751 3 8958 2.638e-15 ***
## Residuals 8960
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Neg.AD_OSK vs Neg.AD_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.99275 19.978 3 8206 6.744e-13 ***
## Residuals 8208
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## $`Neg.CON_GFP vs Neg.AD_GFP`
## Df Wilks approx F num Df den Df Pr(>F)
## Condition 1 0.98926 30.158 3 8334 < 2.2e-16 ***
## Residuals 8336
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 13D density
Only positive
CON: Grey AD: Blue AD OSK: Green
RNA_identity + AD_Engram
AD_Engram + Engram
Compare positive and negative
Positive: Grey Negative: Red
RNA_identity + AD_Engram
AD_Engram + Engram
Engrams
2D
### 3D
Non engrams
2D
Quantification
Cell identity
## Group infected N RNA_identity_score sd se ci
## 1 AD_GFP Neg 3793 0.5383472 0.06338481 0.0010291857 0.002017811
## 2 AD_GFP Pos 1532 0.5300116 0.06206719 0.0015857425 0.003110457
## 3 AD_OSK Neg 4417 0.5386765 0.06307698 0.0009490895 0.001860691
## 4 AD_OSK Pos 1213 0.5403867 0.05938564 0.0017051045 0.003345284
## 5 CON_GFP Neg 4545 0.5293344 0.07653628 0.0011352732 0.002225687
## 6 CON_GFP Pos 1562 0.5434752 0.06571780 0.0016628096 0.003261576## Df Sum Sq Mean Sq F value Pr(>F)
## infected 1 0.02 0.02121 4.739 0.0295 *
## Group 2 0.11 0.05635 12.589 3.44e-06 ***
## infected:Group 2 0.29 0.14298 31.946 1.42e-14 ***
## Residuals 17056 76.34 0.00448
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = RNA_identity_score ~ infected * Group, data = cell_meta)
##
## $infected
## diff lwr upr p adj
## Pos-Neg 0.002566697 0.0002557277 0.004877665 0.0294939
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP 0.003281368 0.0002838615 6.278875e-03 0.0277973
## CON_GFP-AD_GFP -0.002915924 -0.0058559786 2.412974e-05 0.0524836
## CON_GFP-AD_OSK -0.006197293 -0.0090944921 -3.300093e-03 0.0000016
##
## $`infected:Group`
## diff lwr upr p adj
## Pos:AD_GFP-Neg:AD_GFP -0.0083355544 -0.0141074213 -0.002563688 0.0005534
## Neg:AD_OSK-Neg:AD_GFP 0.0003293357 -0.0038914545 0.004550126 0.9999259
## Pos:AD_OSK-Neg:AD_GFP 0.0020395119 -0.0042497677 0.008328792 0.9404157
## Neg:CON_GFP-Neg:AD_GFP -0.0090128413 -0.0132060829 -0.004819600 0.0000000
## Pos:CON_GFP-Neg:AD_GFP 0.0051280059 -0.0006042439 0.010860256 0.1101079
## Neg:AD_OSK-Pos:AD_GFP 0.0086648901 0.0030115357 0.014318244 0.0001829
## Pos:AD_OSK-Pos:AD_GFP 0.0103750664 0.0030470117 0.017703121 0.0007780
## Neg:CON_GFP-Pos:AD_GFP -0.0006772869 -0.0063101033 0.004955530 0.9993798
## Pos:CON_GFP-Pos:AD_GFP 0.0134635603 0.0066076115 0.020319509 0.0000004
## Pos:AD_OSK-Neg:AD_OSK 0.0017101763 -0.0044705200 0.007890873 0.9695410
## Neg:CON_GFP-Neg:AD_OSK -0.0093421770 -0.0133707304 -0.005313623 0.0000000
## Pos:CON_GFP-Neg:AD_OSK 0.0047986702 -0.0008142306 0.010411571 0.1437575
## Neg:CON_GFP-Pos:AD_OSK -0.0110523533 -0.0172142695 -0.004890437 0.0000048
## Pos:CON_GFP-Pos:AD_OSK 0.0030884939 -0.0042083975 0.010385385 0.8340025
## Pos:CON_GFP-Neg:CON_GFP 0.0141408472 0.0085486329 0.019733062 0.0000000## Df Sum Sq Mean Sq F value Pr(>F)
## Group 2 0.151 0.07568 19.26 4.72e-09 ***
## Residuals 4304 16.914 0.00393
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = RNA_identity_score ~ Group, data = cell_meta_pos)
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP 0.010375066 0.004726344 0.016023788 0.0000505
## CON_GFP-AD_GFP 0.013463560 0.008178754 0.018748366 0.0000000
## CON_GFP-AD_OSK 0.003088494 -0.002536206 0.008713194 0.4023676Engram score
## Group infected N Engram sd se ci
## 1 AD_GFP Neg 3793 11.46841 6.881428 0.11173446 0.2190654
## 2 AD_GFP Pos 1532 12.97797 5.113672 0.13064822 0.2562684
## 3 AD_OSK Neg 4417 11.26788 7.147655 0.10754740 0.2108468
## 4 AD_OSK Pos 1213 13.49662 5.194060 0.14913397 0.2925894
## 5 CON_GFP Neg 4545 11.93334 6.681481 0.09910733 0.1942986
## 6 CON_GFP Pos 1562 14.42729 4.390256 0.11108344 0.2178885## Df Sum Sq Mean Sq F value Pr(>F)
## infected 1 13997 13997 335.851 < 2e-16 ***
## Group 2 2131 1065 25.563 8.22e-12 ***
## infected:Group 2 575 288 6.902 0.00101 **
## Residuals 17056 710850 42
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Engram ~ infected * Group, data = cell_meta)
##
## $infected
## diff lwr upr p adj
## Pos-Neg 2.085023 1.862017 2.308029 0
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP -0.00400414 -0.2932603 0.285252 0.9994197
## CON_GFP-AD_GFP 0.73508653 0.4513745 1.018799 0.0000000
## CON_GFP-AD_OSK 0.73909067 0.4595141 1.018667 0.0000000
##
## $`infected:Group`
## diff lwr upr p adj
## Pos:AD_GFP-Neg:AD_GFP 1.5095699 0.95259097 2.0665488 0.0000000
## Neg:AD_OSK-Neg:AD_GFP -0.2005265 -0.60782815 0.2067752 0.7251985
## Pos:AD_OSK-Neg:AD_GFP 2.0282157 1.42130706 2.6351244 0.0000000
## Neg:CON_GFP-Neg:AD_GFP 0.4649387 0.06029543 0.8695820 0.0135381
## Pos:CON_GFP-Neg:AD_GFP 2.9588814 2.40572547 3.5120373 0.0000000
## Neg:AD_OSK-Pos:AD_GFP -1.7100963 -2.25563891 -1.1645538 0.0000000
## Pos:AD_OSK-Pos:AD_GFP 0.5186459 -0.18850347 1.2257952 0.2922958
## Neg:CON_GFP-Pos:AD_GFP -1.0446312 -1.58819186 -0.5010705 0.0000007
## Pos:CON_GFP-Pos:AD_GFP 1.4493115 0.78771986 2.1109031 0.0000000
## Pos:AD_OSK-Neg:AD_OSK 2.2287422 1.63231171 2.8251727 0.0000000
## Neg:CON_GFP-Neg:AD_OSK 0.6654652 0.27671412 1.0542162 0.0000160
## Pos:CON_GFP-Neg:AD_OSK 3.1594078 2.61776898 3.7010467 0.0000000
## Neg:CON_GFP-Pos:AD_OSK -1.5632770 -2.15789529 -0.9686588 0.0000000
## Pos:CON_GFP-Pos:AD_OSK 0.9306656 0.22652350 1.6348077 0.0022914
## Pos:CON_GFP-Neg:CON_GFP 2.4939427 1.95430003 3.0335853 0.0000000## Df Sum Sq Mean Sq F value Pr(>F)
## Group 2 1664 832.1 34.83 9.88e-16 ***
## Residuals 4304 102820 23.9
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Engram ~ Group, data = cell_meta_pos)
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP 0.5186459 0.07822606 0.9590657 0.0159594
## CON_GFP-AD_GFP 1.4493115 1.03726548 1.8613575 0.0000000
## CON_GFP-AD_OSK 0.9306656 0.49211874 1.3692125 0.0000021AD (Engram) score
## Group infected N AD sd se ci
## 1 AD_GFP Neg 3793 6.245809 3.945846 0.06406911 0.1256132
## 2 AD_GFP Pos 1532 6.616369 2.711663 0.06927975 0.1358933
## 3 AD_OSK Neg 4417 5.975718 4.218301 0.06347078 0.1244345
## 4 AD_OSK Pos 1213 5.992133 3.000105 0.08614022 0.1690005
## 5 CON_GFP Neg 4545 5.764117 3.904469 0.05791553 0.1135426
## 6 CON_GFP Pos 1562 5.454999 2.669654 0.06754832 0.1324950## Df Sum Sq Mean Sq F value Pr(>F)
## infected 1 5 4.8 0.343 0.558
## Group 2 1264 632.1 44.890 < 2e-16 ***
## infected:Group 2 260 130.0 9.233 9.83e-05 ***
## Residuals 17056 240183 14.1
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = AD ~ infected * Group, data = cell_meta)
##
## $infected
## diff lwr upr p adj
## Pos-Neg 0.03873784 -0.09089024 0.1683659 0.5580486
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP -0.3703652 -0.5385029 -0.2022275 8.00e-07
## CON_GFP-AD_GFP -0.6661286 -0.8310437 -0.5012135 0.00e+00
## CON_GFP-AD_OSK -0.2957634 -0.4582746 -0.1332522 5.95e-05
##
## $`infected:Group`
## diff lwr upr p adj
## Pos:AD_GFP-Neg:AD_GFP 0.37056032 0.04680173 0.694318914 0.0141208
## Neg:AD_OSK-Neg:AD_GFP -0.27009051 -0.50684530 -0.033335731 0.0146296
## Pos:AD_OSK-Neg:AD_GFP -0.25367538 -0.60645696 0.099106203 0.3143989
## Neg:CON_GFP-Neg:AD_GFP -0.48169151 -0.71690103 -0.246481998 0.0000001
## Pos:CON_GFP-Neg:AD_GFP -0.79080993 -1.11234630 -0.469273557 0.0000000
## Neg:AD_OSK-Pos:AD_GFP -0.64065083 -0.95776176 -0.323539908 0.0000002
## Pos:AD_OSK-Pos:AD_GFP -0.62423570 -1.03528479 -0.213186607 0.0002190
## Neg:CON_GFP-Pos:AD_GFP -0.85225183 -1.16821073 -0.536292931 0.0000000
## Pos:CON_GFP-Pos:AD_GFP -1.16137025 -1.54593773 -0.776802764 0.0000000
## Pos:AD_OSK-Neg:AD_OSK 0.01641513 -0.33027573 0.363106001 0.9999938
## Neg:CON_GFP-Neg:AD_OSK -0.21160100 -0.43757274 0.014370742 0.0816237
## Pos:CON_GFP-Neg:AD_OSK -0.52071941 -0.83556120 -0.205877628 0.0000361
## Neg:CON_GFP-Pos:AD_OSK -0.22801613 -0.57365358 0.117621316 0.4144369
## Pos:CON_GFP-Pos:AD_OSK -0.53713455 -0.94643562 -0.127833475 0.0025411
## Pos:CON_GFP-Neg:CON_GFP -0.30911842 -0.62279984 0.004563012 0.0561362## Df Sum Sq Mean Sq F value Pr(>F)
## Group 2 1044 522.2 67.51 <2e-16 ***
## Residuals 4304 33292 7.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = AD ~ Group, data = cell_meta_pos)
##
## $Group
## diff lwr upr p adj
## AD_OSK-AD_GFP -0.6242357 -0.8748444 -0.3736270 1.0e-07
## CON_GFP-AD_GFP -1.1613702 -1.3958336 -0.9269069 0.0e+00
## CON_GFP-AD_OSK -0.5371345 -0.7866775 -0.2875916 1.4e-06#Save image